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Origin and diversity of alginate lyases of families PL-5 and -7 in Sphingomonas sp. strain A1.

ABSTRACT: Sphingomonas sp. strain A1 has three endotype alginate lyases (A1-I, A1-II [family PL-7], and A1-III [family PL-5]), each of which is encoded by a single gene. In addition to those of these lyases, a gene (the A1-II' gene) showing significant identity with the A1-II gene was present in the bacterial genome and coded for an alginate lyase with broad substrate specificity. Since no expression of A1-II' was observed even in bacterial cells grown on alginate, the A1-II' gene was thought to be a silent gene derived from the A1-II gene, presumably through duplication, modification, and translocation.

SUBMITTER: Miyake O

PROVIDER: S-EPMC387801 | biostudies-literature | 2004 May

REPOSITORIES: biostudies-literature

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Origin and diversity of alginate lyases of families PL-5 and -7 in Sphingomonas sp. strain A1.

Miyake Osamu O Ochiai Akihito A Hashimoto Wataru W Murata Kousaku K

Journal of bacteriology 20040501 9

Sphingomonas sp. strain A1 has three endotype alginate lyases (A1-I, A1-II [family PL-7], and A1-III [family PL-5]), each of which is encoded by a single gene. In addition to those of these lyases, a gene (the A1-II' gene) showing significant identity with the A1-II gene was present in the bacterial genome and coded for an alginate lyase with broad substrate specificity. Since no expression of A1-II' was observed even in bacterial cells grown on alginate, the A1-II' gene was thought to be a sile ...[more]

PMID: 15090531

Similar Datasets

Alginate-dependent gene expression mechanism in Sphingomonas sp. strain A1.

Project description:Sphingomonas sp. strain A1, a Gram-negative bacterium, directly incorporates alginate polysaccharide into the cytoplasm through a periplasmic alginate-binding protein-dependent ATP-binding cassette transporter. The polysaccharide is degraded to monosaccharides via the formation of oligosaccharides by endo- and exotype alginate lyases. The strain A1 proteins for alginate uptake and degradation are encoded in both strands of a genetic cluster in the bacterial genome and inducibly expressed in the presence of alginate. Here we show the function of the alginate-dependent transcription factor AlgO and its mode of action on the genetic cluster and alginate oligosaccharides. A putative gene within the genetic cluster seems to encode a transcription factor-like protein (AlgO). Mutant strain A1 (ΔAlgO mutant) cells with a disrupted algO gene constitutively produced alginate-related proteins. DNA microarray analysis indicated that wild-type cells inducibly transcribed the genetic cluster only in the presence of alginate, while ΔAlgO mutant cells constitutively expressed the genetic cluster. A gel mobility shift assay showed that AlgO binds to the specific intergenic region between algO and algS (algO-algS). Binding of AlgO to the algO-algS intergenic region diminished with increasing alginate oligosaccharides. These results demonstrated a novel alginate-dependent gene expression mechanism. In the absence of alginate, AlgO binds to the algO-algS intergenic region and represses the expression of both strands of the genetic cluster, while in the presence of alginate, AlgO dissociates from the algO-algS intergenic region via binding to alginate oligosaccharides produced through the lyase reaction and subsequently initiates transcription of the genetic cluster. This is the first report on the mechanism by which alginate regulates the expression of the gene cluster.

| S-EPMC4097587 | biostudies-literature

Expression analysis of motile strain of Sphingomonas sp. A1

Project description:Investigation of whole genome gene expression level in motile strain of Sphingomonas. sp A1 All flagellar genes in motile strain of Sphingomonas. sp A1 are highly transcribed.

2014-11-01 | GSE62901 | GEO

Crystallization and preliminary X-ray analysis of alginate importer from Sphingomonas sp. A1.

Project description:Sphingomonas sp. A1 directly incorporates alginate polysaccharides through a 'superchannel' comprising a pit on the cell surface, alginate-binding proteins in the periplasm and an ABC transporter (alginate importer) in the inner membrane. Alginate importer, consisting of four subunits, AlgM1, AlgM2 and two molecules of AlgS, was crystallized in the presence of the binding protein AlgQ2. Preliminary X-ray analysis showed that the crystal diffracted to 3.3 Å resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 72.5, b = 136.8, c = 273.3 Å, suggesting the presence of one complex in the asymmetric unit.

| S-EPMC3310540 | biostudies-literature

Molecular identification of oligoalginate lyase of Sphingomonas sp. strain A1 as one of the enzymes required for complete depolymerization of alginate.

Project description:A bacterium, Sphingomonas sp. strain A1, can incorporate alginate into cells through a novel ABC (ATP-binding cassette) transporter system specific to the macromolecule. The transported alginate is depolymerized to di- and trisaccharides by three kinds of cytoplasmic alginate lyases (A1-I [66 kDa], A1-II [25 kDa], and A1-III [40 kDa]) generated from a single precursor through posttranslational autoprocessing. The resultant alginate oligosaccharides were degraded to monosaccharides by cytoplasmic oligoalginate lyase. The enzyme and its gene were isolated from the bacterial cells grown in the presence of alginate. The purified enzyme was a monomer with a molecular mass of 85 kDa and cleaved glycosidic bonds not only in oligosaccharides produced from alginate by alginate lyases but also in polysaccharides (alginate, polymannuronate, and polyguluronate) most efficiently at pH 8.0 and 37 degrees C. The reaction catalyzed by the oligoalginate lyase was exolytic and thought to play an important role in the complete depolymerization of alginate in Sphingomonas sp. strain A1. The gene for this novel enzyme consisted of an open reading frame of 2,286 bp encoding a polypeptide with a molecular weight of 86,543 and was located downstream of the genes coding for the precursor of alginate lyases (aly) and the ABC transporter (algS, algM1, and algM2). This result indicates that the genes for proteins required for the transport and complete depolymerization of alginate are assembled to form a cluster.

| S-EPMC94629 | biostudies-literature

Expression analysis of motile strain of Sphingomonas sp. A1

Project description:Investigation of whole genome gene expression level in motile strain of Sphingomonas. sp A1 All flagellar genes in motile strain of Sphingomonas. sp A1 are highly transcribed. A two chip study using total RNA recovered from wild-type and motile strains of Sphingomonas. sp A1 grown in 0.5% alginate medium.

2014-11-01 | E-GEOD-62901 | biostudies-arrayexpress

Regulation of pH attenuates toxicity of a byproduct produced by an ethanologenic strain of Sphingomonas sp. A1 during ethanol fermentation from alginate.

Project description:Marine macroalgae is a promising carbon source that contains alginate and mannitol as major carbohydrates. A bioengineered ethanologenic strain of the bacterium Sphingomonas sp. A1 can produce ethanol from alginate, but not mannitol, whereas the yeast Saccharomyces paradoxus NBRC 0259-3 can produce ethanol from mannitol, but not alginate. Thus, one practical approach for converting both alginate and mannitol into ethanol would involve two-step fermentation, in which the ethanologenic bacterium initially converts alginate into ethanol, and then the yeast produces ethanol from mannitol. In this study, we found that, during fermentation from alginate, the ethanologenic bacterium lost viability and secreted toxic byproducts into the medium. These toxic byproducts inhibited bacterial growth and killed bacterial cells and also inhibited growth of S. paradoxus NBRC 0259-3. We discovered that adjusting the pH of the culture supernatant or the culture medium containing the toxic byproducts to 6.0 attenuated the toxicity toward both bacteria and yeast, and also extended the period of viability of the bacterium. Although continuous adjustment of pH to 6.0 failed to improve the ethanol productivity of this ethanologenic bacterium, this pH adjustment worked very well in the two-step fermentation due to the attenuation of toxicity toward S. paradoxus NBRC 0259-3. These findings provide information critical for establishment of a practical system for ethanol production from brown macroalgae.

| S-EPMC4008464 | biostudies-literature

Crystallization and preliminary crystallographic analysis of the cell-surface alginate-binding protein Algp7 isolated from Sphingomonas sp. A1.

Project description:Sphingomonas sp. A1, a Gram-negative bacterium, directly internalizes alginate macromolecules through a mouth-like pit that is present on its cell surface. The alginate-binding protein Algp7, which was found to be localized on the cell surface, contributes to the accumulation of alginate in the pit. Algp7 was crystallized at 293 K by means of the sitting-drop vapour-diffusion method with polyethylene glycol 3350 as a crystallizing agent. Preliminary X-ray analysis showed that the Algp7 crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 50.1, b = 98.0, c = 100.1 A, and that it diffracted to 2.8 A resolution.

| S-EPMC2675599 | biostudies-literature

Expression analysis of Sphingomonas. sp A1 AlgO-deficient mutant grown in 0.5% alginate medium or 0.5% yeast extract medium

2014-01-28 | GSE54410 | GEO

Expression analysis of Sphingomonas. sp A1 AlgO-deficient mutant grown in 0.5% alginate medium or 0.5% yeast extract medium

Project description:Investigation of whole genome gene expression level changes in Sphingomonas. sp A1 AlgO-deficient mutant grown on alginate compared with that on yeast extract AlgO is a possble transcriptional factor described in J. Bacteriol. (2000) 182(14):3998-4004 by Momma K, Okamoto M, Mishima Y, Mori S, Hashimoto W, and Murata K. A two chip study using total RNA recovered from two cultures of Sphingomonas. sp A1 AlgO-deficient mutant grown in 0.5% alginate medium and 0.5% yeast extract medium. Each chip measures the expression level of genes from Sphingomonas. sp A1.

2014-01-28 | E-GEOD-54410 | biostudies-arrayexpress

Diversity of Three-Dimensional Structures and Catalytic Mechanisms of Alginate Lyases.

Project description:Alginate is a linear polysaccharide produced mainly by brown algae in marine environments. Alginate consists of a linear block copolymer made up of two monomeric units, ?-d-mannuronate (M) and its C-5 epimer ?-l-guluronate (G). Alginate lyases are polysaccharide lyases (PL) that degrade alginate via a ?-elimination reaction. These enzymes play an important role in marine carbon recycling and also have widespread industrial applications. So far, more than 1,774 alginate lyase sequences have been identified and are distributed into 7 PL families. In this review, the folds, conformational changes during catalysis, and catalytic mechanisms of alginate lyases are described. Thus far, structures for 15 alginate lyases have been solved and are divided into 3 fold classes: the ?-jelly roll class (PL7, -14, and -18), the (?/?)n toroid class (PL5, -15, and -17), and the ?-helix fold (PL6). These enzymes adopt two different mechanisms for catalysis, and three kinds of conformational changes occur during this process. Moreover, common features in the structures, conformational changes, and catalytic mechanisms are summarized, providing a comprehensive understanding on alginate lyases.

| S-EPMC5772247 | biostudies-literature

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